4) Now GPS start to send at 19200 baud, so you'll see some garbage in RealTerm. Go to Port tab, close link (untick Open button), change baudrate to 19200, and Open link again. If you see valid GPS data, then all is OK:

5) In ArduPilot code, search for line Serial.begin(4800);
and change it to Serial.begin(19200);
Done! You have now faster serial communication in your ArduPilot code. GPS device will remember the baud speed as it has internal battery and memory and keeps the setting.
You're now prepared for more data to be sent by telemetry link.

Michal: very nice! We stuck with 4800 because we wanted it to work "out of the box" but your suggestion is excellent, and a reminder that we should start a "pimp my ArduPilot" section for upgrades like this!

The gps will return to the default state after 3 days of not using it...

I wrote a code long time ago to change the speed of the EM-406, to 38400bps, and switch to the Binary protocol, that is a lot better than the NMEA and reliable.. Then when i try to use it again i've discovered that the unit reset to the default settings after some days of leave it off.

This happens because the unit has a capacitor (not battery). In the other hand ublox saves it settings in the eeprom. The same trick you have post works with locosys, and it really has battery but not binary protocol... :/

Well, and how i change it? is hard close, If was it a battery it suppose to recharge when you plug it (like the capacitor does), but i leave it all day powered when i was developing the code and testing it... The capacitor (like the average of the GPS have), is only for quick fix if you loose power for short periods... For example the paparazzi uBlox uses a capacitor too, and the sparkfun uBlox do not use anything, so if you loose power you need to wait a little bit more than Paparazzi. About the settings do not meters because is saved in the EEPROM. I also have the SIRF3 helix antenna, and you have to connect you own backup battery...

Hmm, I gave it pause today for 8 hours, and settings persisted.
Em604 user guide says: "new parameters will be stored in battery backed SRAM".
I'll post more results after leaving GPS few days unplugged.

As shown in picture above, I made a very temporal connection on cut connector's wires.
Maybe it also works if you plug GPS and FTDI to ArduPilot, and program it as described above, then you don't need to make crazy wiring. But I didn't test if it works that way.